To determine the impact of the species difference between rodents and humans in response to peroxisome proliferators mediated by peroxisome proliferator-activated receptor alpha, PPAR alpha-humanized transgenic mice (hPPAR) were generated In hPPAR alpha PAC mice, the human PPAR alpha gene is expressed in tissues with high fatty acid catabolism and induced upon fasting, similar to mouse PPAR alpha in wild-type mice. Upon treatment with the peroxisome proliferator fenofibrate, hPPARalpha mice exhibited responses similar to wild-type mice, including peroxisome proliferation, lowering of serum triglycerides, and induction of PPARalpha target genes encoding enzymes involved in fatty acid metabolism in liver, kidney, and heart, suggesting that human PPARalpha functions in the same manner as mouse PPAR alpha in regulating fatty acid metabolism and lowering serum triglycerides. However, in contrast to wild-type mice, treatment of hPPARalpha mice with fenofibrate did not cause significant hepatomegaly and hepatocyte proliferation, thus indicating that the mechanisms by which PPAR alpha affects lipid metabolism are distinct from the hepatocyte proliferation response, the latter of which is only induced by mouse PPAR alpha. In addition, a differential regulation of several genes, including the oncogenic let-7C microRNA by peroxisome proliferators, was observed between wild-type and hPPARalpha mice that may contribute to the inherent difference between mouse and human PPAR alpha in activation of hepatocellular proliferation. The hPPARalpha mouse model thus provides an in vivo platform to investigate the species difference mediated by PPARalpha and an ideal model for human risk assessment PPs exposure. To define a set of urinary biomarkers that could be used to determine the efficacy of PPARalpha agonists, a metabolomic investigation was undertaken in wild-type and PPARalpha-null mice fed for 2 weeks either a regular diet or a diet containing the PPARalpha ligand [4-chloro-6-(2,3-xylidino)-2-pyrimidinylthio] acetic acid (Wy-14,643), and their urine was analyzed by ultra-performance liquid chromatography coupled with time-of-flight mass spectrometry. Principal components analysis of 6393 accurate mass positive ions revealed clustering as a single phenotype of the treated and untreated PPARalpha-null mice plus two additional discrete phenotypes for the treated and untreated wild-type mice. Biomarkers of PPARalpha activation were identified from their accurate masses and confirmed by tandem mass spectrometry of authentic compounds. Biomarkers were quantitated from raw chromatographic data using appropriate calibration curves. PPARalpha urinary biomarkers highly statistically significantly elevated by Wy-14,643 treatment included 11beta-hydroxy-3,20-dioxopregn-4-en-21-oic acid (more than 3700-fold), 11beta,20-dihydroxy-3-oxopregn-4-en-21-oic acid (50-fold), nicotinamide, nicotinamide 1-oxide, 1-methylnicotinamide, hippuric acid, and 2,8-dihydroxyquinoline-beta-d-glucuronide. PPARalpha urinary biomarkers highly statistically significantly attenuated by Wy-14,643 treatment included xanthurenic acid (1.3-fold), hexanoylglycine (20-fold), phenylpropionylglycine (4-fold), and cinnamoylglycine (9-fold). These biomarkers arise from PPARalpha effects on tryptophan, corticosterone, and fatty acid metabolism and on glucuronidation. This study underscores the power of mass spectrometry-based metabolomics combined with genetically modified mice in the definition of monogenic metabolic phenotypes. This is the first study of the use of metabolomics to uncover biomarkers for nuclear receptor activation. The most common clinical implication for the activation of the human pregnane X receptor (PXR) is the occurrence of drug-drug interactions mediated by up-regulated cytochromes P450 3A (CYP3A) enzymes. Typical rodent models do not predict drug-drug interactions mediated by human PXR because of species differences in response to PXR ligands. A PXR-humanized mouse model was generated by bacterial artificial chromosome transgenesis in PXR-null mice using a clone containing the complete human PXR gene. In this PXR-humanized mouse, PXR is selectively expressed in the liver and intestine, the same tissue expression pattern as CYP3A. Treatment of PXR-humanized mice with the PXR ligands mimicked the human response, since both hepatic and intestinal CYP3As were strongly induced by rifampicin, a human-specific PXR ligand, but not by pregnenolone 16alpha-carbonitrile, a rodent-specific PXR ligand. All-trans-retinoic acid (ATRA) is an effective treatment for acute promyelocytic leukemia and several solid tumors; however, its use is limited by resistance due to increased metabolism. ATRA resistance is due to autoinduced metabolism regulated by the retinoic acid receptor-CYP26 pathway. However, treatment of cancer is usually not done with a single antineoplastic agent, but with a variety of combined chemotherapy regimens, including several anticancer drugs, and other concomitantly administered supportive drugs. PXR, an orphan nuclear receptor that functions as a ligand-activated transcription factor, serves as an important xenobiotic sensor regulating metabolism and elimination. Many prescription drugs are PXR ligands, which can activate PXR target genes, including phase I enzymes, phase II enzymes, and transporter genes. Due to the marked species differences in response to PXR ligands, Pxr-null, wild-type, and PXR-humanized transgenic mouse models were used. In addition to pregnenolone 16alpha-carbonitrile, several clinically relevant PXR ligands such as rifampicin and dexamethasone, all increased ATRA metabolism both in vitro and in vivo, which was PXR-dependent, and up-regulation of cytochrome P4503a (CYP3A) was the major contributor. Furthermore, induction of the genes encoding several drug transporters was also observed. This study suggested that coadministration of PXR ligands can increase ATRA metabolism through activation of the PXR-CYP3A pathway, which might be a mechanism for some form of ATRA resistance. Other PXR target transporters might also be involved. Colon epithelial cells are critical for barrier function and contain a highly developed immune response. A previous study has shown hypoxia-inducible factor (HIF) as a critical regulator of barrier protection during colon epithelial injury. However, the role of hypoxia-inducible factor signaling in colon mucosal immunity is not known. Intestinal-specific disruption of von Hippel-Lindau tumor suppressor protein hypoxia-inducible factor 1alpha, and aryl hydrocarbon nuclear translocator was generated. Colon inflammation was induced using a dextran sulfate sodium-induced colitis model, and the mice were analyzed. In mice, colonic epithelium disruption of Vhl resulted in constitutive expression of HIF, which initiated an increase in inflammatory infiltrates and edema in the colon. These effects were ameliorated in mice by disruption of both Vhl and Arnt, which inactivates HIF. In a dextran sulfate sodium-induced colitis model, increased HIF expression correlated with more severe clinical symptoms and an increase in histologic damage, while disruption of both Vhl and Arnt in the colon epithelium inhibited these effects. Furthermore, colons with constitutive activation o [summary truncated at 7800 characters]